[English] 日本語
Yorodumi
- EMDB-28333: Cryo-EM structure of human HSP90B in the closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28333
TitleCryo-EM structure of human HSP90B in the closed state
Map dataCryo-EM structure of human HSP90B in the closed state
Sample
  • Complex: HSP90B dimer in the closed AMPPNP bound state
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsHSP90B / AIPL1 / phosphodiesterase 6 / CHAPERONE
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding / protein kinase regulator activity / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / cellular response to interleukin-4 / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / : / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / ESR-mediated signaling / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / tau protein binding / placenta development / Regulation of actin dynamics for phagocytic cup formation / kinase binding / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / double-stranded RNA binding / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex binding / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSrivastava D / Artemyev NO
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY-10843 United States
CitationJournal: Structure / Year: 2023
Title: Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1.
Authors: Dhiraj Srivastava / Ravi P Yadav / Sneha Singh / Kimberly Boyd / Nikolai O Artemyev /
Abstract: Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting ...Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1). Disruption of PDE6 maturation underlies a severe form of retina degeneration. Here, we report a 3.9 Å cryoelectron microscopy (cryo-EM) structure of the complex of HSP90 with AIPL1. This structure reveals a unique interaction of the FK506-binding protein (FKBP)-like domain of AIPL1 with HSP90 at its dimer interface. Unusually, the N terminus AIPL1 inserts into the HSP90 lumen in a manner that was observed previously for HSP90 clients. Deletion of the 7 N-terminal residues of AIPL1 decreased its ability to cochaperone PDE6. Multi-body refinement of the cryo-EM data indicated large swing-like movements of AIPL1-FKBP. Modeling the complex of HSP90 with AIPL1 using crosslinking constraints indicated proximity of the mobile tetratricopeptide repeat (TPR) domain with the C-terminal domain of HSP90. Our study establishes a framework for future structural studies of PDE6 maturation.
History
DepositionOct 2, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28333.png

Downloads & links

-
Map

FileDownload / File: emd_28333.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human HSP90B in the closed state
Voxel sizeX=Y=Z: 1.246 Å
Density
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-11.448881999999999 - 31.791640999999998
Average (Standard dev.)0.0010798957 (±0.96887445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.20001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_28333_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 1

Fileemd_28333_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_28333_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HSP90B dimer in the closed AMPPNP bound state

EntireName: HSP90B dimer in the closed AMPPNP bound state
Components
  • Complex: HSP90B dimer in the closed AMPPNP bound state
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: HSP90B dimer in the closed AMPPNP bound state

SupramoleculeName: HSP90B dimer in the closed AMPPNP bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 174 KDa

-
Macromolecule #1: Heat shock protein HSP 90-beta

MacromoleculeName: Heat shock protein HSP 90-beta / type: protein_or_peptide / ID: 1 / Details: HSP90B / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.170227 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHDYD IPTTGYPYDV PDYAENLYFQ GASPEEVHHG EEEVETFAFQ AEIAQLMSLI INTFYSNKEI FLRELISNAS DALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTLV DTGIGMTKAD LINNLGTIAK SGTKAFMEAL QAGADISMIG Q FGVGFYSA ...String:
MHHHHHHDYD IPTTGYPYDV PDYAENLYFQ GASPEEVHHG EEEVETFAFQ AEIAQLMSLI INTFYSNKEI FLRELISNAS DALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTLV DTGIGMTKAD LINNLGTIAK SGTKAFMEAL QAGADISMIG Q FGVGFYSA YLVAEKVVVI TKHNDDEQYA WESSAGGSFT VRADHGEPIG RGTKVILHLK EDQTEYLEER RVKEVVKKHS QF IGYPITL YLEKEREKEI SDDEAEEEKG EKEEEDKDDE EKPKIEDVGS DEEDDSGKDK KKKTKKIKEK YIDQEELNKT KPI WTRNPD DITQEEYGEF YKSLTNDWED HLAVKHFSVE GQLEFRALLF IPRRAPFDLF ENKKKKNNIK LYVRRVFIMD SCDE LIPEY LNFIRGVVDS EDLPLNISRE MLQQSKILKV IRKNIVKKCL ELFSELAEDK ENYKKFYEAF SKNLKLGIHE DSTNR RRLS ELLRYHTSQS GDEMTSLSEY VSRMKETQKS IYYITGESKE QVANSAFVER VRKRGFEVVY MTEPIDEYCV QQLKEF DGK SLVSVTKEGL ELPEDEEEKK KMEESKAKFE NLCKLMKEIL DKKVEKVTIS NRLVSSPCCI VTSTYGWTAN MERIMKA QA LRDNSTMGYM MAKKHLEINP DHPIVETLRQ KAEADKNDKA VKDLVVLLFE TALLSSGFSL EDPQTHSNRI YRMIKLGL G IDEDEVAAEE PNAAVPDEIP PLEGDEDASR MEEVD

UniProtKB: Heat shock protein HSP 90-beta

-
Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHSPES
200.0 mMNaCl
1.0 mMTCEP

Details: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.032 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 116639
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Details: masked FSC resolution / Number images used: 440225
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM (ver. 1.0)
Final 3D classificationSoftware - Name: cisTEM (ver. 1.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8eob:
Cryo-EM structure of human HSP90B in the closed state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more